COORDINATIONNUMBER
 This is part of the symfunc module It is only available if you configure PLUMED with ./configure –enable-modules=symfunc . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of coordination numbers such as the minimum, the number less than a certain quantity and so on.

So that the calculated coordination numbers have continuous derivatives the following function is used:

$s = \frac{ 1 - \left(\frac{r-d_0}{r_0}\right)^n } { 1 - \left(\frac{r-d_0}{r_0}\right)^m }$

If R_POWER is set, this will use the product of pairwise distance raised to the R_POWER with the coordination number function defined above. This was used in White and Voth [114] as a way of indirectly biasing radial distribution functions. Note that in that reference this function is referred to as moments of coordination number, but here we call them powers to distinguish from the existing MOMENTS keyword of Multicolvars.

Examples

The following input tells plumed to calculate the coordination numbers of atoms 1-100 with themselves. The minimum coordination number is then calculated.

Click on the labels of the actions for more information on what each action computes

The following input tells plumed to calculate how many atoms from 1-100 are within 3.0 of each of the atoms from 101-110. In the first 101 is the central atom, in the second 102 is the central atom and so on. The number of coordination numbers more than 6 is then computed.

Click on the labels of the actions for more information on what each action computes